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Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine
Alexander S Leonard1, Danang Crysnanto2, Zih-Hua Fang2
1Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland. alexander.leonard@usys.ethz.ch.
Nature Communications
|May 31, 2022
Summary
Pangenome construction is robust across sequencing platforms and assembly methods. Haplotype-resolved assemblies improve genome research, revealing numerous structural variants with potential phenotypic impacts.
Area of Science:
- Genomics
- Comparative genomics
Background:
- Pangenomes offer advantages over linear reference assemblies in genome research.
- The impact of sequencing platforms and assembly methods on pangenome construction remains understudied.
Purpose of the Study:
- To evaluate the effects of different sequencing platforms and assembly approaches on pangenome construction.
- To assess the quality of haplotype-resolved assemblies generated from varying levels of heterozygosity.
- To identify structural variants within bovine pangenomes and their potential phenotypic consequences.
Main Methods:
- Generation of haplotype-resolved assemblies from three bovine trios using different sequencing technologies (HiFi, ONT) and coverage depths.
- Construction of structural variant-based pangenomes from these assemblies.
- Analysis of pangenome consensus across different platforms, assemblers, and coverages.
- Identification and annotation of structural variants, particularly those overlapping coding sequences.
Main Results:
- Haplotype-resolved assemblies significantly improve contiguity, completeness, and accuracy compared to the current Bos taurus reference genome.
- Diploid coverage as low as 20x (HiFi) or 60x (ONT) is sufficient for high-quality assemblies meeting Vertebrate Genomes Project standards.
- Pangenomes constructed from these assemblies show strong consensus irrespective of sequencing platform, assembler, or coverage.
- Identification of 90,000 structural variants, including 931 within coding sequences, affecting genes like QRICH2, PRDM9, HSPA1A, TAS2R46, and GC.
Conclusions:
- Pangenome construction is reliable and consistent across various sequencing and assembly strategies.
- Haplotype-resolved assemblies are a powerful tool for advancing genome research and variant discovery.
- The identified structural variants represent potential drivers of phenotypic variation in cattle.
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